title: Divergent leukemia subclones as cellular models for testing vulnerabilities associated with gains in chromosomes 7, 8 or 18

city: Badalona

first: Mar

last: Mallo

address: Ctra de Can Ruti, s/n, camí de les escoles. Edifici IMPPC

institute: Josep Carreras Leukaemia Research Institute

type:
Genome variation profiling by array
Genome variation profiling by SNP array

summary: Hematopoietic malignancies are frequently characterized by karyotypic abnormalities. The development of targeted drugs has been pioneered with compounds against gene products of fusion genes caused by chromosomal translocations. While polysomies are equally frequent as translocations, for many of them we are lacking therapeutic approaches aimed at synthetic lethality. Here, we report two new cell lines, named MBU-7 and MBU-8, that differ in complete trisomies of chromosome 18, a partial trisomy of chromosome 7 and a tetrasomy of the p-arm of chromosome 8, but otherwise share the same mutational pattern and complex karyotype. Both cell lines are divergent clones of U-937 cells and have the morphology and immunoprofile of monocytic cells. The distinct karyotypic differences between MBU-7 and MBU-8 are associated with a difference in the specific response to nucleoside analogues. Taken together, we propose the MBU-7 and MBU-8 cell lines described here as suitable in vitro models for screening and testing vulnerabilities that are associated with the disease-relevant polysomies of chromosome 7, 8 and 18.

overall_design: Two leukemia-derived cell lines were studied

first: Michael

last: Maher

first: Jeannine

last: Diesch

first: Marguerite-Marie

last: Le Pannérer

first: Marta

last: Cabezón

first: Sara

last: Vergara

first: Aleix

last: López

first: Alba

last: Tudel

first: Francesc

last: Solé

first: Isabel

last: Granada

first: Marc

last: Sorigue

first: Lurdes

last: Zamora

first: Marcus

last: Buschbeck


title: Ephexin1 cooperates with K-Ras to promote oncogenic Ras-driven tumorigenesis

status: Public on Oct 27 2021

city: Gwangju

first: Jeeho

last: Kim

address: 309, Pilmun-daero, Dong-gu, Gwangju, Republic of Korea

department: medical school

country: South Korea

institute: chosun university

type: Expression profiling by high throughput sequencing

summary: Ephexin1 was initially identified as a neuronal guanine nucleotide exchange factor involved in the control of neuronal development and synaptic homeostasis. Here, we demonstrate that the induction of Ephexin1 expression by an oncogenic K-Ras mutation amplifies the MAPK signaling via direct interaction with oncogenic Ras and contributes to colon and lung tumorigenesis. Ephexin1 cooperates with mutant Ras to accelerate skin tumorigenesis in vivo. In addition, we have demonstrated that the functionally relevant interaction between oncogenic K-Ras and Ephexin1. Together, these findings suggest that Ephexin1 serves as a positive regulator of Ras-driven oncogenesis and potentially represents a novel target for therapeutic intervention.

overall_design: To determine whether change of mRNA by Ephexin1, we examined in shControl_H1299 cells and shEphexin1_H1299 cells were compared.

first: Hojin

last: You


title: RNA-seq in male and female mouse liver for two mouse strains: C57BL/6J and CAST/EiJ.

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

country: USA

institute: Boston University

summary: Sequencing files provided here are mouse liver RNA-seq in two mouse strains: C57BL/6J and CAST/EiJ. This is part of a larger study published in PLoS Genetics (2021) "Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model" that includes DNase-seq and H3K27ac ChIP-seq in mouse liver from the same two strains. This allows us to identify strain-shared ("core") and strain-unique sex-biased genes and enhancers.

overall_design: RNA-seq in male and female mouse liver, n=5 biological replicates per sex and per strain

first: Bryan

middle: J

last: Matthews


title: Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Gene expression profiling with hypoxia and BRD-K34222889 from primary human pulmonary artery endothelial cells (HPAECs)

city: Pittsburgh

first: Adam

last: Handen

state: Pennsylvania

address: 200 Lothrop Street

department: Vascular Medicine Institute

institute: University of Pittsburgh

summary:
BRD-K34222889 is a structural analog of the anti-inflammatory and senolytic drug piperlongumine. Piperlongumine inhibits GSTP1, an enzyme that places glutathione moieties on cysteine residues of various protein targets and for modulation of protein stability. The objective of this experiment was to determine the effect of a Piperlongumine analog BRD-K34222889 in endothelial dysfunction. Interestingly, BRD-K34222889 was found to inhibit glutathione S-transferase P (GSTP1), which increased ISCU protein stability via preventing glutathionylation and thus increased oxidative metabolism and decreased PAEC apoptosis. Activites of BRD-K34222889 reversed gene transcripts altered in PAECs with hypoxia that more than half of these genes were categorized in pathways relevant to cell cycle, cell death, and metabolism and all known to be controlled by ISCU.
We use Affymetrix Clairom S platform to determine the whole gene expression.

overall_design: HPAECs were induced with hypoxia with or without BRD-K34222889 and appropriate control for 48h. There were three biological replicate for each group for a total of 9 samples. The groups were Normoxia with vehicle, hypoxia with vehicle, hypoxia with BRD-K34222889

first: Stephen

middle: Y

last: Chan

first: Jimin

last: Yang

first: Gil

last: Speyer

middle: L


title: Mouse liver DNase-seq identification of DNase hypersensitive sites (DHS) in male and female mouse liver for two mouse strains: C57BL/6J and CAST/EiJ.

summary: Sequencing files provided here are mouse liver DNase-seq in two mouse strains: C57BL/6J and CAST/EiJ. This is part of a larger study published in PLoS Genetics (2021) "Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model" that includes RNA-seq and H3K27ac ChIP-seq in mouse liver from the same two strains. This allows us to identify strain-shared ("core") and strain-unique sex-biased genes and enhancers.

overall_design: DNase-seq in male and female mouse liver for two mouse strains


title: Mouse liver H3K27ac histone marks in male and female mouse liver for two mouse strains: C57BL/6J and CAST/EiJ.

summary: Sequencing files provided here are mouse liver ChIP-seq for the activating histone mark H3K27ac in two mouse strains: C57BL/6J and CAST/EiJ. This is part of a larger study published in PLoS Genetics (2021) "Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model" that includes RNA-seq and DNase-seq in mouse liver from the same two strains. This allows us to identify strain-shared ("core") and strain-unique sex-biased genes and enhancers.

overall_design: H3K27ac ChIP-seq in male and female mouse liver


title: RNA-seq in human hematopoietic stem cells (HSCs) cultures on 3 different materials

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

summary: Hematopoietic stem cell transplantation (HSCT) is successfully applied since the late 1950s, however, its efficacy still needs to be improved. A promising strategy is to transplant high numbers of pluripotent hematopoietic stem cells (HSCs). Therefore, an advanced ex vivo culture system is needed that supports the proliferation and maintains the pluripotency of HSC to override possible limitations in cell numbers gained from donors. To model the natural HSC niche in vitro and thus, to amplify high numbers of undifferentiated HSCs, we used an optimized HSC cell culture medium in combination with artificial 3D bone marrow-like scaffolds made of polydimethylsiloxane (PDMS). After 14 days in vitro (DIV) cell culture, we performed transcriptome and proteome analysis of the whole cell populations. Ingenuity pathway analysis (IPA) indicated that our 3D PDMS cell culture scaffolds altered PI3K/AKT/mTOR pathways and activated SREBP, HIF1α and FOXO signaling leading to metabolic adaptations, which we confirmed by ELISA, Western blot and metabolic flux analysis. These molecular signaling pathways can promote the expansion HSCs and are involved in their pluripotency maintenance. Thus, we could show that our 3D bone marrow-like PDMS scaffolds activate key molecular signaling pathways to amplify the numbers of undifferentiated HSCs efficiently ex vivo.

overall_design:
16 samples: HSCs of 4 anonymous human indivduals were used. Of each donor, a control sample was take before in vitro amplification ("Day0") while 3 fractions of HSCs were cultured on different materials ("2D PS", "3D PDMS" and "3D SiOn") for 14 days. The study has been approved by the Jena University Hospital Ethics Committee (#3595-10/12, #5320-10/17).
***Please note that raw data is not provided as consent forms do not allow for public access to raw data****

first: Marco

last: Groth

first: Christian

last: Marx

first: Lisa

last: Marx-Blümel


title: Phosphorylated UPF1 (p-UPF1) RIP-seq using mouse Neuro-2A (N2A) neuroblastoma cells

status: Public on Oct 25 2021

city: Rochester

first: Tatsuaki

last: Kurosaki

state: NY

address: 601 Elmwood Avenue, Box 712

department: Biochemistry and Biophysics

institute: University of Rochester

summary: To identify high-confidence NMD targets in mouse N2A neuroblastoma cells, we used our established transcriptome-wide RNA sequencing (RNA-seq) methodologies. Through parallel analyses of RNA-seq upon UPF1-knockdown (KD) and RNA immunoprecipitation (RIP-seq) footprinting of p-UPF1-bound RNAs, we identified 1027 high-confidence neuronal NMD targets.

overall_design: RIP-seq experiments for p-UPF1, control IPs using rabbit IgG, and additional control sample without IP were performed in triplicates.

first: Lynne

middle: E

last: Maquat


title: RNA-seq using mouse Neuro-2A (N2A) neuroblastoma cells

overall_design: RNA profiles of N2A cells treated with control siRNA (siCtl; n=2) or Upf1 siRNA (siUpf1; n=3).


title: NMD abnormalities during brain development in the Fmr1-knockout mouse model of fragile X syndrome

relation:
SuperSeries of: GSE180134
SuperSeries of: GSE180135
SuperSeries of: GSE180136


title: Cataloging human PRDM9 variability utilizing long-read sequencing technologies reveals PRDM9 population-specificity and two distinct groupings of related alleles

status: Public on Oct 26 2021

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

summary: The PRDM9 protein determines sites of meiotic recombination in humans by directing meiotic DNA double strand breaks to specific loci. Targeting specificity is encoded by a long array of C2H2 zinc fingers that binds to DNA. This zinc finger array is hypervariable, resulting in innumerable alleles, each with a potentially different DNA binding preference. Assessment of PRDM9 diversity is important for understanding the complexity of human population genetics, inheritance linkage patterns, and the predisposition to genetic disease. Due to the repetitive nature of the PRDM9 zinc finger array, large-scale sequencing of human PRDM9 is challenging. We therefore developed a long-read sequencing strategy to infer the diploid PRDM9 zinc finger array genotype in a high-throughput manner. From an unbiased study of PRDM9 allelic diversity in 716 individuals from 7 human populations, we detected 70 high-confidence PRDM9 alleles. Several alleles differ in frequency among human populations and 33 alleles had not been identified by previous studies, which were heavily biased to European populations. PRDM9 alleles are distinguished by their DNA binding site preferences and fall into two major categories related to the most common PRDM9-A and PRDM9-C alleles. We also find that inter-conversion between allele types is likely rare. By mapping meiotic DSBs in testis, we find that small variations in PRDM9 can substantially alter the meiotic recombination landscape, demonstrating that minor PRDM9 variants may play an under-appreciated role in shaping patterns of human recombination. In summary, our data greatly expands our knowledge of PRDM9 diversity in humans.

overall_design:
Genotyping of PRDM9 in 7 human populations using amplicon enrichment coupled to long-read sequencing.  DSB hotspot mapping in human males with a variant of the most common PRDM9-A allele.
**Please note that as the raw data need to be processed through a compute-intensive, specialized alignment pipeline, the (extensively processed) BAM files are included as processed data with special exception.

first: Benjamin

last: Alleva

first: Florencia

last: Pratto

first: Mini

last: Huang

first: Rafael

middle: D

last: Camerini-Otero


title: RNA-seq using mouse one-day old (P1) cortical neurons cultured two-days in vitro (2DIV)

summary: RNA-seq of cortical neurons deriving from two-day cultures of P1 cortex revealed that the levels of nonsense-mediated mRNA decay (NMD) targets were generally and significantly decreased in Fmr1-knockout (KO) relative to WT mice.

overall_design: RNA profiles in P1 cortical neurons of wild type (n=3) and Fmr1-KO (n=3) mice.


title: Retinoic acid rewires the adrenergic core regulatory circuitry of neuroblastoma but can be subverted by enhancer hijacking of MYC or MYCN

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research


title: UnAIDed Class-Switching in activated B-cells reveals intrinsic features of a self-cleaving IgH locus

city: Rennes

first: Brice

last: Laffleur

address: 2 avenue du professeur Léon Bernard

country: France

institute: INSERM

summary: Activation-induced deaminase (AID) is the major actor of immunoglobulin (Ig) genes diversification in germinal center B cells. From its first description, it was considered as mandatory for class switch recombination (CSR) and this discovery initiated a long quest for all of the AID-interacting factors controlling its activity. The mechanisms focusing AID-mediated DNA lesions to given target sequences remain incompletely understood, with regards to the detailed characterization of optimal substrates in which cytidine deamination will lead to double strand breaks (DSBs) and chromosomal cleavage. In an effort to reconsider whether such CSR breaks absolutely require AID, we herein provide evidence refuting this dogma in both human and mouse B lymphocytes, based on deep-sequencing approaches. In activated B-cells from either AID-deficient mice or human AID-deficient patients, we report an intrinsic ability of the IgH locus to undergo “on-target” cleavage and subsequent synapsis of broken regions in conditions able to yield low-level CSR. DNA breaks occur in such conditions within the same repetitive S regions usually targeted by AID, but their repair follows a specific pathway with increased usage of microhomology-mediated repair. These data further demonstrate the role of AID machinery as not initiating de novo chromosomal cleavage, but rather catalyzing a process which spontaneously initiates at low levels in an appropriately conformed IgH locus.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mouse and human primary B cells were used to amplify Sµ to Sγ junctions after class switch recombination. DNA was extracted and DNA junctions were amplified by nested PCR to create librairies. Each library was prepared using 200ng PCR2 product. Barcoded libraries with 200-pb read lengths were prepared using Ion Xpress plus Fragment Library Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Each barcoded library was mixed in equal amounts and diluted to 100 pM. Libraries were run on chip 540 on the Ion S5 sequencer (Life Technologies).

first: Iman

last: Dalloul

first: Zeinab

first: Batoul

last: Webbe

first: Florence

last: Jouan

first: Baptiste

last: Brauge

first: Paco

last: Derouault

first: Jeanne

last: Moreau

first: Sven

last: Kracker

first: Alain

last: Fischer

first: Anne

middle: H

last: Durandy

first: Sandrine

last: Le Noir

first: Michel

last: Cogné


title: Epigenomic profiling by optimized ChIL-seq for tissue

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

summary: We optimized the epigenomic profiling technology ChIL-seq for tissue. We confirmed the "ChIL for tissue" has sufficient sensitivity, specificity and reproducibility, in identification of enhancers, transcription factors, transcriptional activation genes in a single-thin-section of tissues.

overall_design: The targets of ChIL-seq are the transcription factor: Hnf4alpha, histone modification: H3K27ac and RNA Polymerase II. The tissues were profiled using single cryo-sections from human breast cancer, mouse liver, heart, testis, and cardiotoxin-injured muscle for regeneration study. The RNA-seq data of the tissues were obtained.

first: Kazumitsu

last: Maehara

first: Kaori

last: Tanaka

first: Akihito

last: Harada


title: CCR2-dependent monocyte-derived cells restrict SARS-CoV-2 infection

status: Public on Oct 23 2021

city: Atlanta

first: Mehul

last: Suthar

state: GA

address: 2015 Uppergate Dr

department: Department of Pediatrics

institute: Emory University School of Medicine

summary: SARS-CoV-2 has caused a historic pandemic of respiratory disease (COVID-19) and current evidence suggests severe disease is associated with dysregulated immunity within the respiratory tract1,2. However, the innate immune mechanisms that mediate protection during COVID-19 are not well defined. Here we characterize a mouse model of SARS-CoV-2 infection and find that early CCR2-dependent infiltration of monocytes restricts viral burden in the lung. We find that a recently developed mouse-adapted MA-SARS-CoV-2 strain, as well as the emerging B.1.351 variant, trigger an inflammatory response in the lung characterized by expression of pro-inflammatory cytokines and interferon-stimulated genes. Using intravital antibody labeling, we demonstrate that MA-SARS-CoV-2 infection leads to increases in circulating monocytes and an influx of CD45+ cells into the lung parenchyma that is dominated by monocyte-derived cells. scRNA-seq analysis of lung homogenates identified a hyper-inflammatory monocyte profile. We utilize this model to demonstrate that mechanistically, CCR2 signaling promotes infiltration of classical monocytes into the lung and expansion of monocyte-derived cells. Parenchymal monocyte-derived cells appear to play a protective role against MA-SARS-CoV-2, as mice lacking CCR2 showed higher viral loads in the lungs, increased lung viral dissemination, and elevated inflammatory cytokine responses. These studies have identified a CCR2-monocyte axis that is critical for promoting viral control and restricting inflammation within the respiratory tract during SARS-CoV-2 infection.

overall_design: 8 samples in total corresponding to different mice. 4 samples are from mock, control mice. 4 samples are from SARS-CoV-2 infected mice.

first: Abigail

last: Vanderheiden

first: Jeronay

last: Thomas

first: Jacob

last: Kohlmeier

first: Steven

last: Bosinger


title: RNA-sequencing of Influenza A.Cali09 specific CD4+ T cells from healthy UK adults

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: Bulk RNA sequencing of sorted A.Cali09-specific CD4+CD45RA- cells from before and seven days after trivalent seasonal influenza vaccination in healthy UK adults of 18-36 years old and over 65 years old.

overall_design: Samples from before and after vaccination were stained with HLADR0701 or HLADR1101 tetramers loaded with influenza peptides specific to the A.Cali09 strain and antigen experienced CD4+CD45RA- T cells sorted by flow cytometry from day 0 and day 7 after vaccination. On day 7, cells were sorted as being CXCR5+ and PD1 expressing circulating Tfh cells. Between 40 and 1000 cells were sorted per sample directly into lysis buffer for subsequent sequencing with the SmartseqV4 kit from Takara Clontech.

first: Danika

last: Hill

first: Michelle

last: Linterman


title: Expression data from FedEV uptake mesothelial cells

status: Public on Oct 22 2021

city: Baltimore

first: Fumiya

last: Ito

state: MARYLAND

address: 725 N. Wolfe Street, 119 Hunterian

department: Cell Biology

institute: Johns Hopkins University

summary: Asbestos-associated diseases remain a social burden worldwide.  Our previous studies identified asbestos-induced iron-rich milieu for mesothelial cells with ceaseless macrophage ferroptosis.  However, molecular mechanisms how this mutagenic milieu influences mesothelial cells have not been elucidated yet.  Here, we propose a novel mechanism that extracellular vesicles (EVs) mediate asbestos-associated mutagenic factors to mesothelial cells.  In a mice model of intraperitoneal crocidolite injection, mutagenic milieu highly expressed CD63, an exosomal marker.  We then used a CD63-GFP labeled THP-1 macrophage model exposed to crocidolite/iron, which generated EVs under ferroptotic process.  We observed that MeT-5A mesothelial cells can receive and internalize these EVs.  Furthermore, we comprehensively analyzed the ferroptosis-dependent EVs (FedEVs) for transported proteins and identified ferritin heavy/light chains as major proteins.  Therefore, we inferred that FedEVs transport iron from ferroptotic macrophages to mesothelial cells.  RNA sequencing revealed that the mesothelial cells receiving higher amounts of the FedEVs were mitotic, especially at the S and G2/M phases, by the use of Fucci mesothelial cells.  Nuclear 8-hydroxy-2`-deoxyguanosine and γ-H2AX were significantly increased in the recipient mesothelial cells after exposure to FedEVs.  Collectively, we here demonstrate a novel mechanism that FedEVs act as a key mutagenic mediator by transporting iron, which contribute to asbestos-induced mesothelial carcinogenesis.

overall_design:
Examination of 3 different EV uptake in human mesothelial cell-MeT-5A
NT: FedEV (-)
Low: FedEV(+) - GFP low level (FACS)
High: FedEV(+) - GFP high level (FACS)

first: Katsuhiro

last: Kato

first: Shinya

last: Toyokuni


title: Retinoic acid rewires the adrenergic core regulatory circuitry of neuroblastoma but can be subverted by enhancer hijacking of MYC or MYCN (ChIP-Seq)

first: Richard

last: Young

summary: Neuroblastoma cell identity depends on a core regulatory circuit (CRC) of transcription factors that incorporate MYCN to drive the oncogenic gene expression program. For neuroblastomas dependent on the adrenergic CRC, treatment with retinoids can inhibit cell growth and induce differentiation in both primary neuroblastomas and cell lines; however, the underlying mechanisms remain unclear. Here we show that when MYCN-amplified neuroblastomas cells are treated with all-trans retinoic acid (ATRA), they undergo modifications of histone H3K27 acetylation and methylation that decommission super-enhancers driving the expression of PHOX2B and GATA3, together with the activation of new super-enhancers that drive high levels of expression of MEIS1, HIC1 and SOX4. These findings indicate that treatment with ATRA can reprogram the enhancer landscape to collapse the adrenergic CRC, which downregulates MYCN expression, while upregulating a new “retino-sympathetic” CRC that causes proliferative arrest and sympathetic differentiation.  Thus, we provide mechanisms that account for the beneficial effects of retinoids against high-risk neuroblastoma and explain the rapid downregulation of expression of MYCN despite massive levels of gene amplification.

overall_design: ChIP-Seq against transcription factors or H3K27ac-modified histones in neuroblastoma cell lines treated with all-trans retionoic acid

first: Mark

middle: W

last: Zimmerman

first: Adam

last: Durbin

first: Shuning

last: He

first: Alla

last: Berezovskaya

last: Oppel

first: Hui

last: Shi

first: Ting

last: Tao

first: Zhaodong

last: Li

first: Yu

last: Liu

first: Jinghui

last: Zhang

first: Brian

last: Abraham

first: A

middle: T

last: Look


title: Skeletal muscle myonuclei-specific ChIP-Seq of H3K4me3 and H3K27ac

city: Oslo

first: Mads

last: Bengtsen

address: Blindernveien 31

country: Norway

institute: University of Oslo

summary: Skeletal muscle is a heterogeneous tissue. To study the myo-specific epigenetic landscape in the slow soleus and fast extensor digitorum longus (EDL) muscle, myonuclei were purified with PCM1 -an endogenous mark specific for mature myonuclei. Chromatin immunoprecipitation sequencing (ChIP-Seq) was performed using antibodies against the histone marks H3K4me3 and H3K27ac. Comparison of the differently enriched areas between the two muscles shows that the epigenetic landscape reflects the functional properties of the muscles, each with a distinct regulatory program involving distal regulatory enhancers.

overall_design: Mapping of the myo-specific epigenetic landscape in mouse soleus and EDL by ChIP-Seq using antibodies against the two histone marks H3K4me3 and H3K27ac.

first: Ivan

last: Winje

first: Einar

last: Eftestøl

first: Kristian

last: Gundersen


title: Monocyte exhaustion mediated by TRAM

city: Blacksburg

first: Liwu

state: VA

address: 1015 Life Science Cir

institute: Virginia Tech

summary: We performed single cell sequencing analysis of exhausted monocytes generated in vitro through prolonged incubation with high dose LPS.  We demonstated that 5-day prolonged stimulation of WT but not TRAM KO monocytes with high dose LPS drastically induced monocyte exhaustion, as reflected in higher levels of inflammatory marker genes such as CD38 and immuno-suppressor genes including PD-L1.

overall_design: WT or TRAM KO murine monocytes were treated with either PBS or 100 ng/ml LPS for a 5 day period. Treated cells were harvested and used to perform single cell sequencing analysis.

first: Kisha

last: Pradhan

first: Ziyue

last: Yi


title: Nucleosome accessibility in CUTLL3 cell line treated with Vehicle or Pitavastatin and 3 ETP-ALL patients

status: Public on Oct 21 2021

city: New York

first: Marissa

last: Rashkovan

address: 1130 Saint Nicholas Avenue

institute: Columbia University

summary: Analysis of nucleosome accessibility in CUTLL3 ETP-ALL cells following treatment with Vehicle or Pitavastatin for 48 hours and ETP-ALL patients at diagnosis

overall_design:
ATAC-seq from CUTLL3 cells treated with Vehicle or Pitavastatin for 48 hours and 3 patient samples was analyzed
Note from submitter: ATAC-seq fastq files are not present as they contain genomic data about patient samples.

first: Adolfo

last: Ferrando


title: Integrated genomic and proteomic analyses identify stimulus-dependent distinct molecular changes associated with skeletal muscle wasting

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Skeletal muscle wasting is a debilitating condition that occurs with aging and with many diseases, but the underlying mechanisms are incompletely understood. Previous work determined that common transcriptional changes occur in skeletal muscle during atrophy induced by different stimuli. However, whether this holds true at the proteome level remains largely unexplored. Here, we find that, contrary to this earlier model, distinct atrophic stimuli (corticosteroids, cancer, and aging) induce largely different mRNA and protein changes during muscle wasting in mice. Moreover, there is widespread transcriptome-proteome disconnect. Consequently, atrophy markers (atrogenes) identified in earlier microarray-based studies do not emerge from these proteomic surveys as the most relevantly associated with atrophy. Based on these analyses, we identify atrophy-regulated proteins (here defined as “atroproteins”) such as the myokine CCN1/Cyr61, which we find regulates myofiber type switching during sarcopenia. Altogether, these integrated analyses indicate that different catabolic stimuli induce muscle wasting via largely distinct mechanisms.

overall_design: RNA-sequencing data from tibialis anterior muscles from male C57BL/6J mice: old versus young; dexamethasone-treated versus control; LLC cancer versus control; and Cyr61 siRNAs vs NT siRNAs.

first: Liam

middle: C

last: Hunt

first: Flavia

last: Graca

first: Vishwajeeth

last: Pagala

first: Yiping

last: Fan

first: Myriam

last: Labelle

first: Junmin

last: Peng

first: Fabio

last: Demontis


title: RNA-seq in CUTLL3 cell line treated with Vehicle or Pitavastatin

summary: Analysis of RNA-seq gene expression signatures in CUTLL3 ETP-ALL cells following treatment with Vehicle or Pitavastatin for 48 hours

overall_design: RNA-seq from CUTLL3 cells treated with Vehicle or Pitavastatin for 48 hours was analyzed in triplicate


title: RNA-seq in CUTLL1 and CUTLL3 cell lines

summary: Analysis of RNA-seq gene expression signatures in CUTLL3 ETP-ALL and CUTLL1 T-ALL cell lines

overall_design: RNA-seq from CUTLL1 (n=2), CUTLL3 (n=3) samples was analyzed


title: Dementia subtype prediction models constructed by penalized regression methods for multiclass classification using serum microRNA expression data

city: Obu

first: Yuya

last: Asanomi

state: Aichi

address: 7-430 Morioka-cho

institute: National Center for Geriatrics and Gerontology

summary: There are many subtypes of dementia, and identification of diagnostic biomarkers that are minimally-invasive, low-cost, and efficient is desired. Circulating microRNAs (miRNAs) have recently gained attention as easily accessible and non-invasive biomarkers. We conducted a comprehensive miRNA expression analysis of serum samples from 1348 Japanese dementia patients, composed of four subtypes—Alzheimer’s disease (AD), vascular dementia, dementia with Lewy bodies (DLB), and normal pressure hydrocephalus—and 246 control subjects. We used this data to construct dementia subtype prediction models based on penalized regression models with the multiclass classification. We constructed a final prediction model using 46 miRNAs, which classified dementia patients from an independent validation set into four subtypes of dementia. Network analysis of miRNA target genes revealed important hub genes, SRC and CHD3, associated with the AD pathogenesis. Moreover, MCU and CASP3, which are known to be associated with DLB pathogenesis, were identified from our DLB-specific target genes. Our study demonstrates the potential of blood-based biomarkers for use in dementia-subtype prediction models. We believe that further investigation using larger sample sizes will contribute to the accurate classification of subtypes of dementia.

overall_design: Serum samples from 84 patients of normal pressure hydrocephalus (NPH)

first: Daichi

last: Shigemizu

first: Shintaro

last: Akiyama

first: Takashi

last: Sakurai

first: Kouichi

last: Ozaki

first: Takahiro

last: Ochiya

first: Shumpei

last: Niida


title: Bulk RNAseq of AML and endothelial cells in untreated and cytokine-treated conditions

city: Palo Alto

first: Rebecca

last: Richards

state: CA

address: 1000 Welch Rd

department: Pediatrics

institute: Stanford University

summary: We report the use of bulk RNAseq of AML and endothelial cell lines in four conditions (1. Untreated; 2. IFNg - 10 ng/ml; 3. TNFa - 10 ng/ml; 4. IFNg and TNFa - 10 ng/ml) in order to identify genes that are differentially expressed between the two cell types, both at baseline and in an inflammatory microenvironment.

overall_design: mRNA profiles of AML and endothelial cells at baseline and after 24h exposure to proinflammatory cytokines IFNg and/or TNFa

first: Katherine

last: Murphy


title: CALR frameshift mutations accelerate maturation of megakaryocytes in MPN patient-derived iPS cells

city: Aachen

first: Steffen

last: Koschmieder

state: Nordrhein-Westfalen

address: Pauwelsstraße 30

department: Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation

institute: RWTH Aachen

summary: In this dataset, we compare the gene expression data of induced pluripotent stem (iPS) cell-derived CD61+ megakaryocytes carrying heterozygous or homozygous Calreticulin (CALR) ins5 mutations or the CALR wildtype gene.

overall_design: 9 samples; Three biological replicates were analyzed per genotype. Het - heterozygous CALRins5 mutation; Hom - homozygous CALR mutation; WTcr - CALR wildtype generated by CRISPR/Cas9 using the respective mutated clone.

first: Kathrin

last: Olschok

first: Lijuan

last: Han

first: Marcelo

last: de Toledo

first: Janik

last: Böhnke

first: Martin

last: Graßhoff

first: Ivan

middle: G

last: Costa

first: Alexandre

last: Theocharides

first: Angela

last: Maurer

first: Herdit

middle: M

last: Schüler

first: Eva

last: Buhl

first: Kristina

last: Pannen

first: Julian

last: Baumeister

first: Milena

last: Kalmer

first: Siddharth

last: Gupta

first: Peter

last: Boor

first: Deniz

last: Gezer

first: Tim

last: Brümmendorf

last: Zenke

first: Nicolas

last: Chatain


title: H3K27acetylation ChIP-seq in CUTLL3 cell line treated with Vehicle or Pitavastatin

first: Marissa

last: Rashkovan

summary: Analysis of H3K27Ac in CUTLL3 ETP-ALL cells following treatment with Vehicle or Pitavastatin for 48 hours

overall_design: ChIP-seq from CUTLL3 cells treated with Vehicle or Pitavastatin for 48 hours was analyzed

first: Adolfo

last: Ferrando


title: Metabolic profiling of ETP-ALL

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Genome-wide analysis of effects of ARID1A depletion in mouse embryonic stem cells

status: Public on Oct 24 2021

city: Dundee

first: Tom

last: Owen-Hughes

state: Tayside

address: Dow Street

department: School of Lifesciences, Gene Regulation and Expression

institute: University of Dundee

summary: A degron system is used to deplete ARID1A a subunit of the SWI/SNF complex in mouse embryonic stem cells. Genome wide analysis of chromatin accessibility (ATAC-seq), nucleosome posistioning (MNase-seq),  nascent transcription (TT-seq), binding to EP300 and presence of histone H3 K27acetylation (ChIP-seq) amd histone H3K27 tria-methylation (ChIP-seq) allowed us to identify two different pathways responsible for the up and downregulation of transcription following the loss of ARID1A. The rapid depletion of ARID1A generates mini domains of nucleomes at pluripotency transcription factor binding sites. Loss of ARID1A also results in the redistribution of the co-activator EP300. Locations of co-incident EP300 dissociation and lost chromatin accessibility occur adjacent to rapidly downregulated genes. Promoter proximal regions that gain EP300 are linked to genes that are transcriptionally upregulated. Our findings illustrate the importance of both direct and indirect effects in causing rapid changes to gene expression. Only a few genes are directly affected after ARID1A depletion and contribute to pathways associated with cancer and pluripotency establishing the loss of ARID1A phenotype.

overall_design: We performed a time course (0h, 2h, 6h, 18, 54h, 162h) for the depletion of the ARID1A subunit of the SWI/SNF complex using the TIR1/Auxin-inducible-degron system in mouse embryonic stem cells (E14). Genome wide analysis was performed for the change in chromatin accessibility (ATAC-seq, 3 replicates per time point), nucleosome positioning (MNase-seq, 6 replicates for time point 0h and 2h),  nascent transcription (Transient Transcriptome TT-seq, 4 replicates per time point), binding to EP300 (ChIP-seq, 4 replicates for time point) and presence of histone H3 K27acetylation (ChIP-seq, 4 replicates per time point) and histone H3K27 tri-methylation before and after ARID1A depletion. In addition TT-seq and ATAC-seq also performed for the untagged control cell lines ET905 (time points 0h, 2h, 18h)  and the knock out ARID1A cell line.

first: Nicola

last: Wiechens

first: Seraina

last: Blümli

first: David

last: Clarke


title: Single cell RNA-sequencing of long-term human control and C9ORF72 ALS/FTD patient-specific iPSC-derived cortical organoid slice cultures

first: Lea

middle: Marion Denise

last: Wenger

address: Robinson Way

department: Clinical Neurosciences

institute: University of Cambridge

summary: Single cell RNA sequencing data was collected from 150 day old human cortical organoid slice cultures grown at the air-liquid interface (ALI-COs) from control and ALS/FTD patient-specific induced pluripotent stem cell (iPSC) lines harbouring the C9ORF72 hexanucleotide repeat expansion mutation. Data collection included ALI-COs derived from the following iPSC lines: WTSli042-B (WTS42b) and A18945 (EpiC) for healthy controls, CS30iALS-C9nxx (CS30) and CS29iALS-C9nxx (CS29) for ALS/FTD, and CS29iALS-C9n1.ISOxx (ISO29), a mutation-corrected isogenic line. A total of 148,223 cells were processed over two batches.

overall_design: Single cell RNA-sequencing data was generated using the 10X Genomics Chromium Single Cell 3' Chip and workflow.

first: Kornelia

last: Szebenyi

first: George

last: Gibbons

first: Andras

last: Lakatos


title: Dysregulated lncRNA and mRNA may promote the progression of ischemic stroke via immune and inflammatory pathways: results from RNA sequencing and bioinformatics analysis

status: Public on Oct 20 2021

city: Changchun

first: Yingshuang

last: Wang

state: Jilin

address: NO.1163 Xinmin Street

country: China

institute: Jilin University School of Public Health

type: Non-coding RNA profiling by high throughput sequencing

summary: Long non-coding RNAs (lncRNAs) are widely involved in gene transcription regulation and which act as epigenetic modifiers. To determine whether lncRNAs are involved in ischemic stroke (IS), we analyzed the expression profile of lncRNAs and mRNAs in IS. RNA sequencing was performed on the blood of three pairs of IS patients and heathy controls. Differential expression analysis was used to identify differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs). Based on the co-expression relationships between lncRNA and mRNA, a series of bioinformatics analysis including GO and KEGG enrichment analysis and PPI analysis, were conducted to predict the function of lncRNA. RNA sequencing produced a total of 5 DElncRNAs and 144 DEmRNAs. Influenza A pathway and Herpes simplex infection pathway were the most significant pathway. EP300 and NFKB1 were the most important target proteins, Human leucocyte antigen (HLA) family were the key gene in IS. Analysis of this study revealed that dysregulated lncRNAs in IS may lead to IS by affecting the immune and inflammation system. Findings may be the foundation for understanding the potential role of lncRNAs.

overall_design: LncRNA profile of the peripheral blood of three IS patients and three healthy controls was obtained by RNA sequencing.

first: Feifei

last: Feng

first: Pingping

last: Zheng

first: Lijuan

first: Yanjun

first: Yaogai

last: Lv

first: Li

last: Shen

first: Kexin

last: Li

first: Tianyu

first: Yang

last: Chen

first: Zhigang

last: Liu

first: Yan

last: Yao


title: The Single Cell Sequencing of Immune Cells in malignant pleural effusion

status: Public on Oct 15 2021

city: Beijing

first: Mingming

last: Shao

state: State...

address: 8 Gongren Tiyuchang Nanlu

institute: Beijing Chao-Yang Hospital

summary: By using 10X genomics single-cell RNA sequencing plat, we employed malignant pleural effusion as research model to performed single-cell RNA sequencing to map the immune microenvironment of MPE. Meanwhile we performed TCR and BCR sequencing for immune receptor repertoire analysis.

overall_design: single  cell RNA profiles of 5 paired blood and malignant pleurai effusion samples

first: Huanzhong

last: Shi

first: Kan

last: Zhai

first: Zhongyin

last: Huang


title: scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies

status: Public on Oct 14 2021

city: Munich

first: Binder

last: Elisabeth

address: Kraepelinstr. 2+10

institute: Max-Planck-Institute Psychiatry

summary: Single cell RNA-seq has revolutionized transcriptomics by providing cell type resolution for differential gene expression and expression quantitative trait loci (eQTL) analyses. However, efficient power analysis methods for single cell data and inter-individual comparisons are lacking. Here, we present scPower; a statistical framework for the design and power analysis of multi-sample single cell transcriptomic experiments. We modelled the relationship between sample size, the number of cells per individual, sequencing depth, and the power of detecting differentially expressed genes within cell types. We systematically evaluated these optimal parameter combinations for several single cell profiling platforms, and generated broad recommendations.  In general, shallow sequencing of high numbers of cells leads to higher overall power than deep sequencing of fewer cells. The model, including priors, is implemented as an R package and is accessible as a web tool. scPower is a highly customizable tool that experimentalists can use to quickly compare a multitude of experimental designs and optimize for a limited budget.

overall_design: We performed 10X single cell RNA seq on PBMCs of pools of a total of 14 human study participants. The goal of the experiment was to benchmark different pooling and demultiplexing strategies for multisample single cell transcriptomics experiments. We performed 3 runs of sequencing on a pool of all 14 samples with targeted 8000 cells each. In addition we performed one run with overloading the 10X reaction with 25000 cells. Finally, for assesing the precision of the demultiplexing we split the pool into samples 1-7 and 8-14.

first: Katharina

last: Schmid

first: Barbara

last: Höllbacher

first: Cristiana

last: Cruceanu

first: Anika

last: Böttcher

first: Heiko

last: Lickert

first: Elisabeth

middle: B

last: Binder

first: Fabian

last: Theis

first: Matthias

last: Heinig


title: Triple-negative breast cancer cells rely on kinase-independent functions of CDK8 to evade NK-cell-mediated tumor surveillance

city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

department: Pharmacology / Toxikology

country: Austria

institute: University of Veterinary Medicine Vienna

summary: Triple-negative breast cancer (TNBC) is an aggressive malignant disease that is responsible for approximately 15% of breast cancers. The standard of care relies on surgery and chemotherapy but the prognosis is poor and there is an urgent need for new therapeutic strategies. Recent in silico studies have revealed an inverse correlation between recurrence-free survival and the level of cyclin- dependent kinase 8 (CDK8) in breast cancer patients. CDK8 is known to have a role in natural killer (NK) cell cytotoxicity, but its function in TNBC progression and immune cell recognition or escape has not been investigated. We have used a murine model of orthotopic breast cancer to study the tumor-intrinsic role of CDK8 in TNBC. Knockdown of CDK8 in TNBC cells impairs tumor regrowth upon surgical removal and prevents metastasis. In the absence of CDK8, the epithelial-to-mesenchymal transition (EMT) is impaired and immune-mediated tumor-cell clearance is facilitated. CDK8 drives EMT in TNBC cells in a kinase-independent manner. In vivo experiments have confirmed that CDK8 is a crucial regulator of NK-cell-mediated immune evasion in TNBC. The studies also show that CDK8 is involved in regulating the checkpoint inhibitor programmed death-ligand 1 (PD-L1). The CDK8–PD-L1 axis is found in mouse and human TNBC cells, underlining the importance of CDK8-driven immune cell evasion in these highly aggressive breast cancer cells. Our data link CDK8 to PD-L1 expression and provide a rationale for investigating the possibility of CDK8-directed therapy for TNBC.

overall_design: E0771 cells were retrovirally infected with two independent CDK8 targeting shRNAs and a non-targeting Renilla control shRNA and treated in triplicates either with 1 microMolar Senexin B for 48 hours or with DMSO as a control.

first: Vanessa

last: Knab

first: Dagmar

last: Gotthardt

first: Klara

last: Klein

first: Reinhard

last: Grausenburger

first: Gerwin

last: Heller

first: Ingeborg

last: Menzl

first: Daniela

last: Prinz

first: Jana

last: Trifinopoulos

first: Julia

last: List

last: Fux

first: Agnieszka

last: Witalisz-Siepracka


title: Genetic and epigenetic characterization of posterior pituitary tumors

status: Public on Oct 19 2021

city: Berlin

first: Simone

last: Schmid

address: Charitéplatz 1

department: Department of Neuropathology

institute: Charité-Universitätsmedizin Berlin

type: Methylation profiling by genome tiling array

summary: Pituicytoma (PITUI), granular cell tumor (GCT), and spindle cell oncocytoma (SCO) are rare tumors of the posterior pituitary lobe. Histologically, they may be challenging to distinguish and have been proposed to represent a histological spectrum of a single entity. We performed targeted next-generation sequencing, DNA methylation profiling, and copy number analysis on 47 tumors (14 PITUI; 12 GCT; 21 SCO) to investigate molecular features and explore possibilities of clinically meaningful tumor subclassification.   We detected two main epigenomic subgroups by unsupervised clustering of DNA methylation data, though the overall methylation differences were subtle. The largest group (n=23) contained most PITUIs and a subset of SCOs and was enriched for pathogenic mutations within genes in the MAPK/PI3K pathways (12/17 [71%] of sequenced tumors: FGFR1 (3), HRAS (3), BRAF (2), NF1 (2), CBL (1), MAP2K2 (1), PTEN (1)) and two with TERT promoter mutation. The second group (n=16) contained most GCTs and a subset of SCOs, which mostly lacked identifiable genetic drivers. Outcome analysis demonstrated that the presence of chromosomal imbalances is significantly associated with reduced progression-free survival especially within the combined PITUI and SCO group (p= 0.031).   In summary, we observed only subtle DNA methylation differences between posterior pituitary tumors, indicating that these tumors may be best classified as subtypes of a single entity. Nevertheless, our data indicate differences in mutation patterns and clinical outcome. For a clinically meaningful subclassification, we propose a combined histo-molecular approach into three subtypes: One subtype is defined by granular cell histology, has low mutation rates and favorable outcome. The other two subtypes have SCO or PITUI histology but are separated by chromosomal copy number profile into a favorable group (no copy number changes) and a less favorable group (copy number imbalances present). Both of the latter groups have recurrent MAPK alterations that represent potential therapeutic targets.

overall_design: Bisulphite converted tumor DNA of 47 patients were hybridised to the Illumina Infinium 450k or 850k Human Methylation Beadchip

first: David

last: Capper


title: A LysR-Type Transcriptional Regulator Controls Multiple Phenotypes in Acinetobacter baumannii

first: Philip

middle: N

last: Rather

state: Georgia

address: 1510 Clifton Rd.

department: Department of Microbiology and Immunology

institute: Emory University

summary: Acinetobacter baumannii is a multidrug-resistant, Gram-negative nosocomial pathogen that exhibits phenotypic heterogeneity resulting in virulent opaque (VIR-O) and avirulent translucent (AV-T) colony variants. Each variant has a distinct gene expression profile resulting in multiple phenotypic differences. Cells interconvert between the VIR-O and AV-T variants at high frequency under laboratory conditions, suggesting that the genetic mechanism underlying the phenotypic switch could be manipulated to attenuate virulence. Therefore, our group has focused on identifying and characterizing genes that regulate this switch, which led to the investigation of ABUW_1132 (1132), a highly conserved gene predicted to encode a LysR-type transcriptional regulator. ABUW_1132 was shown to be a global regulator as the expression of 74 genes was altered > 2-fold in an 1132 deletion mutant. The 1132 deletion also resulted in a 16-fold decrease in VIR-O to AV-T switching, loss of 3-OH-C12-HSL secretion, and reduced surface-associated motility. Further, the deletion of 1132 in the AV-T background caused elevated capsule production, which increased colony opacity and altered the typical avirulent phenotype of translucent cells. These findings distinguish 1132 as a global regulatory gene and advance our understanding of A. baumannii’s opacity-virulence switch.

overall_design: A. baumannii cultures of wild-type VIR-O (control) and a mutant for the gene ABUW_1132 were grown in LB media to an OD600 of 0.5.  Gene expression was measured via RNA-sequencing for three biological replicates per sample.

first: Aimee

middle: P

last: Tierney

first: Chui

last: Chin

middle: S

last: Weiss


title: Defective autophagy and increased apoptosis contribute toward the pathogenesis of FKRP-associated muscular dystrophies

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

summary: Fukutin-related protein (FKRP) is a glycosyltransferase involved in glycosylation of alpha-dystroglycan (a-DG). Mutations in FKRP are associated with muscular dystrophies (MD) ranging from limb-girdle LGMDR9 to Walker-Warburg syndrome (WWS), a severe type of congenital MD. Although hypoglycosylation of a-DG is the main hallmark of this group of diseases, a full understanding of the underlying pathophysiology is still missing. Here, we investigated molecular mechanisms impaired by FKRP mutations in pluripotent stem (PS) cell-derived myotubes. FKRP deficient myotubes show transcriptome alterations in genes involved in extracellular matrix receptor interactions, calcium signaling, PI3K-Akt pathway, and lysosomal function. Accordingly, using a panel of patient-specific LGMDR9 and WWS induced PS cell-derived myotubes, we found a significant reduction in the autophagy-lysosome pathway for both disease phenotypes. Additionally, we show that WWS myotubes display decreased ERK1/2 activity and increased apoptosis, which were restored in gene edited myotubes. Our results suggest the autophagy-lysosome pathway and apoptosis may contribute to the FKRP-associated MD pathogenesis.

overall_design: Gene expression profilling was performed in triplicate from human iPSC-derived myotubes.

first: Carolina

last: Ortiz-Cordero

first: Neha

last: Dhoke

first: Rita

last: Perlingeiro


title: Neuronal HSF-1 activity coordinates fat desaturation across tissues in C. elegans via TGF-b/BMP signalling

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

institute: MRC Laboratory of Molecular Biology

summary: To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process that has been previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, the neuronal over-expression of the master regulator of the conserved heat shock response (HSR), Hsf-1, causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase expression in the gut, and a shift in the saturation levels of fatty acids in the plasma membrane, in line with ectothermic adaptive responses. We have identified the cGMP receptor TAX-2/TAX-4 and TGF-β/BMP signalling, as key players in signalling across tissues. We also find that gradual increments in ambient temperature result in HSR activation exclusively in wild-type head neurons. This is the first study to suggest that a thermostat-based mechanism can non-cell autonomously coordinate membrane fluidity in response to warm temperatures across tissues in multicellular animals.

overall_design: RNA-seq comparison between young adult N2 (WT) and AGD1289 (neuronal over-expression of HSF-1)

first: L

last: Chauve

first: S

last: Murdoch

first: F

last: Masoudzadeh

last: Hodge

first: A

last: Lopez-Clavijo

first: H

last: Okkenhaug

first: G

last: West

last: Segonds-Pichon

last: Kienberger

first: M

last: Wakelam

first: O

last: Casanueva


title: Phenotypic plasticity and genetic rewiring underlie adaptation in response to hypomorphic alleles of an essential gene

city: SIngapore

first: Giulia

last: Rancati

address: Biomedical Grove

department: SRIS

country: Singapore

institute: A*STAR

summary: Adaptive evolution in response to cellular stress is a critical process implicated in a wide range of core biological and clinical phenomena. Two major routes of adaptation have been identified: non-genetic cellular plasticity, which allows expression of different phenotypes in novel environments, and genetic variation achieved by selection of fitter phenotypes. While these processes are now broadly accepted, their temporal and epistatic features in the context of cellular evolution and emerging drug resistance are contentious. In this manuscript, we generated hypomorphic alleles of the essential nuclear pore complex (NPC) gene NUP58. By dissecting both early and long-term mechanisms of adaptation in independent clones, we observed that early physiological adaptation correlated with transcriptome rewiring and upregulation of genes known to interact with the NPC. In contrast, long-term adaptation and fitness recovery occurred via focal amplification of NUP58 and restoration of mutant protein expression. These data support the concept that plasticity-mediated and genetic routes can co-exist to enable cellular evolution, with early flexibility of phenotype allowing later acquisition of genetic adaptations to a specific impairment. We propose this approach as a genetic model to mimic targeted drug therapy in human cells and dissection of early and late adaptation. Targeting both mechanisms in parallel may reduce the emergence of drug resistance

overall_design: 4 experimental replicates for NUP58 mutant and control cell lines (6 NUP58 mutants and 2 controls derived from HAP1 cell line/1 NUP58 mutant and 3 controls derived from HCT116 cell line)

first: Hyung-Won

last: Choi

first: Joseph

last: Lee

first: Altea

last: Targa


title: CHD8 safeguards early neuroectoderm differentiation in human ESCs and protects from apoptosis during neurogenesis

city: WuHan

first: Song

last: Ding

address: Donghu Road, No. 115

department: Medical Research Insitiute

institute: Wuhan University

summary: To understand the function of CHD8 in human ESC and neural differentiation, we generated the CHD8 knockout human ESCs and characterize the effect of loss-of-function of CHD8 on pluripotency maintenance and neuroectoderm determination by utilizing an efficient neuroectoderm differentiation protocol. Samples from hESC, CHD8KO_hESC and their derived-neural progenitor cells (hNPC) were collected for high-throughput sequencing with at least two replicates for each sample. Differentially expressed genes analysis showed loss of CHD8 affect the genes in ESC and NPC.

overall_design: We performed RNA-seq using hESCs and hESC-derived neural progenitor cells (hNPC) and CHD8 KO hESCs and CHD8 KO hESC-derived neural progenitor cells (hESC four replicates and the others two replicates).

first: Xianchun

last: Lan

first: Wei

last: Jlang


title: Sepsis leads to lasting changes in phenotype and function of memory CD8 T cells (RNA-Seq)

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

summary: Determine genome-wide open chromatin in P14 memory CD8 T cells 30 days after septic insult

overall_design: A small number of naïve P14 CD8 T cells (Thy1.1) were adoptively transferred into congenically distinct (Thy1.2) wild type hosts to generate P14 chimeras. P14 chimeric mice were then infected with LCMV-Armstrong. 30-days post infection mice underwent sham or CLP surgery. Memory P14 CD8 T cells were isolated and sorted 30-days post surgery (60-days post-infection) for analysis.

first: Vladimir

last: Badovinac


title: Sepsis leads to lasting changes in phenotype and function of memory CD8 T cells


title: The proline and serine rich protein PROSER1 mediates O-GlcNAcylation of TET2 to regulate DNA demethylation on UTX-dependent enhancers and CpG islands [WGBS]

status: Public on Oct 13 2021

first: Wojciech

last: Rosikiewicz

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

type: Methylation profiling by high throughput sequencing

summary: DNA methylation at enhancers and CpG islands usually leads to gene repression, which is counteracted by DNA demethylation through the TET protein family. However, how TET enzymes are recruited and regulated at these genomic loci is not fully understood. Here, we identify TET2 and a previously undescribed proline and serine rich protein, PROSER1 as interactors of UTX, a component of the enhancer-associated MLL3/4 complexes. Affinity purification of PROSER1 resulted in the identification of OGT and TET1-3. We find that PROSER1 mediates the interaction between OGT and TET2, thus promoting TET2 O-GlcNAcylation and protein stability. Additionally, PROSER1, UTX, OGT, and TET1/2 colocalize on many genomic elements genome-wide. Loss of PROSER1 results in lower enrichment of UTX, and TET1/2 at enhancers and CpG islands, with a concomitant increase in DNA methylation and transcriptional downregulation of associated target genes and increased DNA hypermethylation encroachment at H3K4me1-predisposed CpG islands. Taken together, this study describes for the first time a regulator of TET2 O-GlcNAcylation and its implications in mediating DNA demethylation at UTX-dependent enhancers and CpG islands.

overall_design: Identify differentially methylated regions between WT and PROSER1 KO

first: Xiaokang

last: Wang

first: Yurii

last: Sedkov

first: Tanner

last: Martinez

first: Baranda

last: Hansen

first: Patrick

last: Schreiner

first: Beisi

last: Xu

first: Shondra

last: Pruett-Miller

first: Kristian

last: Helin

first: Hans-Martin

last: Herz


title: The proline and serine rich protein PROSER1 mediates O-GlcNAcylation of TET2 to regulate DNA demethylation on UTX-dependent enhancers and CpG islands.


title: Sepsis leads to lasting changes in phenotype and function of memory CD8 T cells (ATAC-Seq)


title: The proline and serine rich protein PROSER1 mediates O-GlcNAcylation of TET2 to regulate DNA demethylation on UTX-dependent enhancers and CpG islands [hMeDIP-seq]

overall_design: Identify if 5hmC was reduced in PROSER1 KO cells at enhacers and CpG islands.


title: The proline and serine rich protein PROSER1 mediates O-GlcNAcylation of TET2 to regulate DNA demethylation on UTX-dependent enhancers and CpG islands [RNA-seq]

overall_design: Identify differentially expressed genes between WT and PROSER1 KO.


title: Nonylphenol treatment effect on RNA expression in colorectal cancer cell line

status: Public on Oct 11 2021

city: Zunyi

first: Xue-feng

last: Yang

address: The Second Affiliated Hospital of Zunyi Medical University, Xinpu New District, Zunyi City, Guizhou Province

institute: The Second Affiliated Hospital of Zunyi Medical College

summary: Nonylphenol (NP) is a common environmental estrogen that has been shown to enhance the proliferation of colorectal cancer (CRC) cells. RNA sequencing was used to explore the differentially expressed genes after NP exposure.

overall_design: COLO205 cells were treated with nonylphenol (NP, 10-6 M) or DMSO  for 24 h.

first: Jing


title: The proline and serine rich protein PROSER1 mediates O-GlcNAcylation of TET2 to regulate DNA demethylation on UTX-dependent enhancers and CpG islands [ChIP-seq]

overall_design: Identify if loss of PROSER1 would affect the localization of UTX, TET proteins, OGT, H3K4 mono, di, tri-methylation, and  H3K27ac at enhancers and CpG islands


title: Brain areas involved with obsessive-compulsive disorder present different DNA methylation modulation

city: São Paulo

first: Caroline

middle: Perez

last: Camilo

state: São Paulo

address: Rua Doutor Ovídio Pires de Campos, 785

department: Institute of Psychiatry

country: Brazil

institute: University of São Paulo

summary:
Background: Obsessive-compulsive disorder (OCD) is characterized by intrusive thoughts and repetitive actions, that presents the involvement of the cortico-striatal areas. The contribution of environmental risk factors to OCD development suggests that epigenetic mechanisms may contribute to its pathophysiology. DNA methylation changes and gene expression were evaluated in post-mortem brain tissues of the cortical (anterior cingulate gyrus and orbitofrontal cortex) and ventral striatum (nucleus accumbens, caudate nucleus and putamen) areas from eight OCD patients and eight matched controls.
Results: There were no differentially methylated CpG (cytosine-phosphate-guanine) sites (DMSs) in any brain area, nevertheless gene modules generated from CpG sites and protein-protein-interaction (PPI) showed enriched gene modules for all brain areas between OCD cases and controls. All brain areas but nucleus accumbens presented a predominantly hypomethylation pattern for the differentially methylated regions (DMRs). Although there were common transcriptional factors that targeted these DMRs, their targeted differentially expressed genes were different among all brain areas. The protein-protein interaction network based on methylation and gene expression data reported that all brain areas were enriched for G-protein signaling pathway, immune response, apoptosis and synapse biological processes but each brain area also presented enrichment of specific signaling pathways. Finally, OCD patients and controls did not present significant DNA methylation age differences.
Conclusions: DNA methylation changes in brain areas involved with OCD, especially those involved with genes related to synaptic plasticity and the immune system could mediate the action of genetic and environmental factors associated with OCD.

overall_design:
Genome-wide DNA methylation analysis in postmortem brain tissues of the cortical (anterior cingulate gyrus and orbitofrontal cortex) and ventral striatum (nucleus accumbens, caudate nucleus and putamen) areas from OCD patients and matched controls, using the Illumina Infinium Human Methylation 450K BeadChips.

Contributor: Biobank for Aging Studies Group (BASG)

first: Kátia

last: de Oliveira

first: Vinícius

last: Gastaldi

first: Arthur

last: Feltrin

first: Bianca

last: Lisboa

first: Vanessa

middle: J

last: de Paula

first: Ariane

last: Moretto

first: Beny

last: Lafer

first: Marcelo

middle: Q

last: Hoexter

first: Euripedes

last: Miguel

first: Mariana

last: Maschietto

first: Helena

last: Brentani


title: Caveolin-1 and Sox-2 are Predictive Biomarkers of Cetuximab Response in Head and Neck Cancer

status: Public on Oct 12 2021

city: Los Angeles

first: Mehdi

last: Bouhaddou

address: 611 Charles E Young Drive, Boyer Hall 530

institute: UCLA

summary: Expression analysis (RNA-seq) and RPPA data (see publication) of head and neck cancer patient-derived xenographs (PDXs) revealed Sox-2 and Cav-1 expression to be biomarker determinants of head and neck cancer patient tumor response to cetuximab (EGFR inhibitor) treatment.

overall_design: Total RNA was extracted from 69 whole PDX tumors using the RNAeasy kit (Qiagen) following manufacturer’s instructions (only 65 were retained for downstream analyses). Total RNA was enriched for poly-A transcripts and sequenced using the NovaSeq 6000 platform (100PE) at the QB3-Berkeley Genomics center at UC Berkeley. Following sequencing, the unaligned reads contained a mix of human stroma, mouse germline, viral and ostensibly other sequences. Hence, prior to mapping to human reference and expression counting, reads were classified to a probable source. For convenience, each sample had been previously split between two fastq files. Adapters were trimmed and reads failing QC removed using fastp (v0.20.0). Reads were classified as "human," "mouse," "both," "neither" and "ambiguous" using Xenome (v1.0.0), a k-mer index based pseudoaligner, with each sample's split files classified independently of each other. Only reads classified as uniquely human progressed to the human expression pipeline. Uniquely human reads were merged into a single fastq file for each sample and next aligned against a ribosomal reference using bwa, removing rRNA matches. Finally, remaining reads were mapped against an Ensembl GRCh38.90 reference. Expression counts were estimated using RSEM (v1.3.1) (see processed TPM file).

first: Jennifer

middle: R

last: Grandis

first: Nevan

last: Krogan

first: Aaron

last: Hechmer

first: Ritu

last: Roy

first: Adam

last: Olshen


title: Mammalian SWI/SNF chromatin remodeler is essential for reductional meiosis in males

city: Chapel hill

first: Terry

last: Magnuson

state: NC

address: 120 Mason Farm Road, Genetics Medicine Bldg.,

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: CUT&RUN to map ARID2 and BRG1 genomic associations  in  late prophase-I and metaphase-I spermatocytes

overall_design: CUT&RUN was performed on prophase-I and metaphase-I spermatocyte enriched populations isolated from P28 and P28.5 testes displaying synchronized spermatogenesis

first: Debashish

last: Menon


title: Comparative gene expression in adult SVZ-neurospheres differentiated under standard conditions and upon manipulations of Pax6 (OE) and/or Pbx1 (KD/OE)

city: Luxembourg

first: Ann-Christin

last: Hau

address: 1, Rue Louis Rech

department: National Center of Pathology

country: Luxembourg

institute: Laboratoire National de sante

summary: We used microarrays to detail the global programme of gene expression underlying neuronal differentiation of SVZ-neurospheres when manipulating Pax6 expression in the presence or absence of Pbx1

overall_design: Freshly isolated stem- and progenitor cells from the SVZ of adult mice were subjected to four treatment regimes: i) infection with pCLIG, GFP-expressing retroviral vector viruses (vector ctrl), ii) infection with pCLIG expressing Pbx1 (Pbx1 OE), iii) transfection with non-targeting siRNAs followed by infection with pCLIG expressing Pax6 (Pax6 OE) and iv) transfection with siRNAs targeting Pbx1 followed by infection with pCLIG expressing Pax6 (Pax6 OE / Pbx1 KD). 48 hours later, the cells were differentiated for 10 hours on laminin-coated dishes by removal of EGF and FGF2 from the culture medium.

first: Dorothea

last: Schulte


title: Real-time quantitative PCR analysis of mouse lungs after exposure to SARS-CoV-2 and variants of concern (VOC)

status: Public on Oct 10 2021

city: Silver Spring

first: Hang

last: Xie

state: Maryland

address: 10993 New Hampshire Ave WO 52/72 Rm 1324

institute: US Food and Drug Administration, Center for Biologics Evaluation and Research

summary: Age-matched K18-hACE2 transgenic mice were infected intranasally with different SARS-CoV-2 viruses, including (1) USA-WA1/2020 (WA) of lineage A, (2) New York-PV09158/2020 (NY) of lineage B.1.3, (3) USA/CA_CDC_5574/2020 (CA) of lineage B.1.1.7 and (4) hCoV-19/South Africa/KRISP-EC-K005321/2020 (SA) of lineage B.1.351.  Mouse lungs were harvested on 3 days post infection (dpi). Total RNA was extracted using QIAgen RNeasy Plus Mini Kit and was reverse transcribed using the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific). Resultant cDNA was used as the template along with RT2 SYBR Green ROX qPCR Mastermix (Qiagen) to perform RT² Profiler™ PCR Array Mouse Hypoxia Signaling Pathway (Qiagen) real-time PCR in Stratagene MX3000p qPCR system.

overall_design: qPCR gene expression profiling.  Lung homogenates from 4-5 SARS-CoV-2 infected K18-hACE2 transgenic mice on dpi 3 were treated as indicated in the summary.  Total RNA extracted was analyzed individually.

first: Peter

last: Radvak


title: MeRIP Sequencing of Lung Tissues from OVA‐induced Acute Allergic Asthma Mice

city: Shanghai

first: Fangzhou

last: Teng

address: No. 12, Urumchi Middle Road, Jingan District

department: Department of Integrative Medicine

institute: Huashan Hospital, Fudan University

summary: The objective of the study was to present a transcriptome-wide m6A methylome profile of lung tissues in mouse model of ovalbumin(OVA)-induced acute allergic asthma.

overall_design: We performed MeRIP-seq and RNA-seq on three lung tissue samples of OVA-induced asthma mice and three lung tissue samples of PBS-induced control mice to explore m6A modification patterns in asthma.

first: Ying

last: Wei

first: Jingcheng

last: Dong


title: Extracellular vesicles in serum and central nervous system tissues contain microRNA signatures in sporadic amyotrophic lateral sclerosis

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

summary: Amyotrophic lateral sclerosis (ALS) is a terminal neurodegenerative disease. Clinical and molecular observations suggest that ALS pathology originates at a single site and spreads in an organized and prion-like manner, possibly driven by extracellular vesicles. Extracellular vesicles transfer cargo molecules associated with ALS pathogenesis, such as misfolded and aggregated proteins and dysregulated microRNAs (miRNAs). However, it is poorly understood whether altered levels of circulating extracellular vesicles or their cargo components reflect pathological signatures of the disease. In this study, we used immuno-affinity-based microfluidic technology, electron microscopy, and NanoString miRNA profiling to isolate and characterize extracellular vesicles and their miRNA cargo from frontal cortex, spinal cord, and serum of sporadic ALS (n=15) and healthy control (n=16) participants. We found larger extracellular vesicles in ALS spinal cord versus controls and smaller sized vesicles in ALS serum. However, there were no changes in the number of extracellular vesicles between cases and controls across any tissues. Characterization of extracellular vesicle-derived miRNA cargo in ALS compared to controls identified significantly altered miRNA levels in all tissues; miRNAs were reduced in ALS frontal cortex and spinal cord and increased in serum. Two miRNAs were dysregulated in all three tissues: miR-342-3p was increased in ALS, and miR-1254 was reduced in ALS. Additional miRNAs overlapping across two tissues included miR-587, miR-298, miR-4443, and miR-450a-2-3p. Predicted targets and pathways associated with the dysregulated miRNAs across the ALS tissues were associated with common biological pathways altered in neurodegeneration, including axon guidance and long-term potentiation. A predicted target of one identified miRNA (N-deacetylase and N-sulfotransferase 4; NDST4) was likewise dysregulated in an in vitro model of ALS, verifying potential biological relevance. Together, these findings demonstrate that circulating extracellular vesicle miRNA cargo mirror those of the central nervous system disease state in ALS, and thereby offer insight into possible pathogenic factors and diagnostic opportunities.

overall_design: NanoString nCounter® Human v3 miRNA miRNA Expression Assays was used to characterize extracellular vesicles and their miRNA cargo from frontal cortex, spinal cord, and serum of sporadic ALS (n=15) and healthy control (n=16) participants.

first: Eva

middle: L

last: Feldman


title: Gene expression profiling of Drosophila melanogaster larval brains after chronich alcohol exposure

city: San Juan

first: Alfredo

last: Ghezzi

state: Puerto Rico

address: PO box 23360

department: Department of Biology

institute: University of Puerto Rico, Rio Piedras

summary: We sequenced mRNA extracted from brains of (1) D. melanogaster larvae exposed to food containing 5% ethanol (v/v) for 6 conscutive days, and (2) an age-matched untreated control larvae, that grew in regular food. Differential gene expression between the two groups was calculated and reported. Each group consisted of 3 biological replicates of 30 brains each.

overall_design: Examination of mRNA levels in brains of D. melanogaster larvae after chronich ethanol exposure was performed using next generation sequencing (NGS) technology (RNA-seq).

first: Ghezzi

last: Alfredo


title: RNA-Seq analysis of HCV long-term infection cells

status: Public on Oct 09 2021

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary: We performed RNA-seq analysis to study the long-term and short-term effects of HCV infection induced gene regulation and expression on virus and host cell interactions.

overall_design: Examination of mRNA profile of short-term HCV (S-HCV), early long-term HCV (eL-HCV) and long-term HCV (L-HCV) on host cell gene expression

first: Shu-Chi

last: Wang


title: Gene signatures detect damaged LSECs in all chronic liver diseases.

status: Public on Oct 08 2021

city: Brussels

first: Stefaan

last: Verhulst

address: Laarbeeklaan 103, D022

department: BMWE

country: Belgium

institute: Vrije Universiteit Brussel

summary: Transcriptional alterations in LSECs from healthy and damaged livers were determined using RNA Sequencing. Models include acute liver injury (1 ip injection of CCl4) with different timepoints during recovery. Illumina NextSeq 500 High was used for sequencing.

overall_design: Bulk RNA sequencing of isolated BalbC mouse LSECs after following injury:  1 injection CCl4 + 1 day (n = 2), 1 injection CCl4 + 3 days (n = 4), 1 injection CCl4 + 7days (n = 4), healthy (non-injected) (n = 4).

first: S

first: E

middle: A

last: van Os

first: L

last: van Grunsven


title: Comparison of viral RNA–host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2

city: Beijing

first: Wenze

last: Huang

address: Tsinghua street

institute: Tsinghua University

summary: We profiled vRNA-host protein interactomes for three RNA virus pathogens (SARS-CoV-2, Zika, and Ebola viruses) using ChIRP-MS. Comparative interactome analyses discovered both common and virus-specific host responses and vRNA-associated proteins that variously promote or restrict viral infection. In particular, SARS-CoV-2 binds and hijacks the host factor IGF2BP1 to stabilize vRNA and augment translation. Our interactome-informed drug repurposing efforts identified several FDA-approved drugs (e.g., Cepharanthine) as broad-spectrum antivirals in cells and hACE2 mice. A co-treatment comprising Cepharanthine and Trifluoperazine was highly potent against the newly emerged SARS-CoV-2 B.1.351 variant. Thus, our study illustrates the scientific and medical discovery utility of adopting a comparative vRNA-host protein interactome perspective.

overall_design: We mapped direct protein-RNA interaction sites using ultraviolet crosslinking and affinity purification (uvCLAP), a CLIP-like technology.

first: Qiangfeng

last: Zhang

first: Shaojun


title: Sperm epigenetic alterations contribute to inter- and transgenerational effects of paternal exposure to long-term psychological stress via evading offspring embryonic reprogramming

first: Xiaoguo

last: Zheng

address: 145 Guangyuan Road

institute: Shanghai Jiaotong University

summary:
Purpose: Paternal life experiences impact offspring health via germline, and epigenetic inheritance provides a potential mechanism. However, global reprogramming during offspring embryogenesis and gametogenesis represents the largest hurdle to conceptualize it. Yet, detailed characterization of how sperm epigenetic alterations carrying “environmental memory” can evade offspring embryonic reprogramming remains elusive.
Methods: we profiled the sperm DNA methylation patterns of three consecutive generations (F0, F1 and F2) in both control and stress groups by using whole-genome bisulfite sequencing (WGBS). A total of 18 sperm samples were analyzed, including three biological replicates for each generation under each treatment. In addition, small RNA sequencing was carried out on paternal sperm samples to investigate whether long-term psychological stress affected the enrichment of certain sncRNAs and to identify whether they participated in mediating the occurrence and paternal inheritance of the stress-induced DMRs
Rsults: Using an optimized data analysis workflow, we obtained approximately 800 million clean reads per sample (build mm10) with strand-specific coverage ~21×, and the data covered ~96.00% of the total 21,867,837 reference CpG dinucleotides. A total of 24,427, 7,975, and 5,173 differentially methylated regions (DMRs) between control and stress groups were found in the F0, F1, and F2 generations, respectively. Inter- and transgenerational inheritance of paternal DMRs were at frequencies approximately 11.36% and 0.48%, respectively. These DMRs related to genes with functional implications for psychological stress response, and tissue inheritance of these DMRs passed paternal disorders epigenetically to offspring. More importantly, these DMRs evaded offspring embryonic reprogramming through erasure and subsequent reestablishment, but not via un-erasure way. Nonetheless, their reestablishment proportions in the primitive streak (E7.5) stage were altered. Furthermore, sncRNA-seq revealed that stress-induced tsRNA, miRNA and rsRNA dysregulation in paternal sperm might play important roles in DMRs occurrence and paternal inheritance.

overall_design:
a total of 18 sperm samples: Control and stress groups, three generations (F0,F1 and F2), three replicates.
12 embryo smaples: Control and stress groups, two generations (F1 and F2), three stages (E3.5: ICM, E7.5: Primitive streak and E13.5: PGCs);  1 oocyte sample derived from maternal strain (DBA/2J)

first: Zhenhua

last: Li

first: Guishuan

first: Hanshu

first: Yuchuan

last: Zhou

first: Xinzhi

last: Zhao

first: C

middle: Y

first: Yunbo

last: Qiao

first: Fei

last: Sun


title: Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites

first: Jiayong

last: Yin

state: Shanghai

address: Fenglin street

department: Institutes of Biomedical Sciences

institute: Fudan University

summary: 8-Oxo-7,8-dihydro-2’-deoxyguanosine (OG), one of the most common oxidative DNA damages, causes genome instability and is associated with cancer, neurological diseases and aging. In addition, OG and its repair intermediates can regulate gene transcription, and thus play a role in sensing cellular oxidative stress. However, the lack of methods to precisely map OG has hindered the study of its biological roles. Here we developed a single-nucleotide resolution OG-sequencing method, named CLAPS-seq (Chemical Labeling And Polymerase Stalling Sequencing), to measure the genome-wide distribution of both exogenous and endogenous OGs with high specificity. Our data identified decreased OG occurrence at G-quadruplexes (G4s), in association with underrepresentation of OGs in promoters which have high GC content. Furthermore, we discovered that potential quadruplex sequences (PQSs) were hotspots of OGs which may in turn stimulate the formation of G4s at PQSs, implying a role of non-G4-PQSs in OG-mediated oxidative stress response.

overall_design:
We detected 8-oxodG under different conditions in HeLa cells, each group had 2 or 3 biological replicates.
For sample titles, WT refers to Endo(endogenous), VITRO refers to Exo-N(exogenous-naked) and VIVO refers to Exo-C(exogenous-cellular).

first: Jiao

last: An

first: Mengdie

first: Sizhong

last: Wu

first: Christopher

last: Selby

first: Yanyan

last: Yang

first: Aziz

last: Sancar

first: Guoliang

last: Xu

first: Maoxiang

last: Qian

first: Jinchuan

last: Hu


title: Nucleolar and spindle associated protein 1 enhances chemoresistance through DNA damage repair pathway in chronic lymphocytic leukemia by binding with RAD51

city: Jinan

first: Yang

last: Han

state: Shandong

address: No.324, Jingwu Road

institute: Shandong Provincial Hospital

summary:
Purpose: Nucleolar and spindle associated protein 1 (NUSAP1), serves as a microtubule binding protein in chromosome separation, spindle assembly, and plays significant role to ensure normal regulation of cell cycle as well. This experiment aimed to document the NUSAP1 expression and functions in chronic lymphocytic leukemia (CLL).
Methods: Lentivirus vectors either encoding shNUSAP1 or empty lentiviral vector were stably transfected into MEC-1 cells. 3 shNUSAP1 transfected and 3 shControl transfected MEC-1 cell samples were performed RNA sequencing (RNA-seq) analysis, functional enrichment analyses of gene ontology (GO) and gene set enrichment analysis (GSEA).
Results: Silencing NUSAP1 inhibited the cell proliferation, promoted cell apoptosis and G0/G1 phase arrest. Mechanistically, high expression of NUSAP1 strengthened DNA damage repairing with RAD51 engagement. Our results also indicated that NUSAP1 knockdown suppressed the growth of CLL cells in vivo.
Conclusion: Our research investigates the mechanism by which NUSAP1 enhances chemoresistance via DNA damage repair signaling by stabilizing RAD51 in CLL cells. Hence, NUSAP1 may be expected to be a perspective target for the treatment of CLL with chemotherapy resistance.

overall_design: RNA profiles of three test and three control samples were generated by deep sequencing, using Illumina HiSeq 4000.

first: Y

first: X

last: Yun

first: J

last: Liu

first: Z

last: Tian

last: Wang


title: Foetal-specific contributors to infant MLL-AF4-driven Acute Lymphoblastic Leukaemia

status: Public on Oct 07 2021

city: Edinburgh

first: Katrin

last: Ottersbach

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: University of Edinburgh

summary: As MLL-rearranged infant leukaemia is known to initiate in utero, we sought to identify developemntal genes expressed in foetal cells that may aid leukaemogenesis. Bulk RNA-Seq was therefore carried out on mouse and human foetal liver blood progenitors (lymphoid-primed multipotent progenitors [LMPPs] and haematopoietic stem cells/ multipotent progenitor cells [HSC/MPPs]) and compared with the same cell types isolated from developmentally later human cord blood and mouse adult bone marrow.

overall_design: For the human samples, HSC/MPPs (CD34+ CD38- CD45RA-) and LMPPs (CD34+ CD38- CD45RA+) were sorted from 13-19 week old foetal livers, and HSC/MPPs from cord blood.  For the mouse samples, LMPPs (Lin- Sca1+ ckit+ CD45+ B220- CD19- Flt3+) were sorted from wild-type, VEC-Cre+ controls and Mll-AF4-expressing E14.5 foetal livers and from wild-type 8-10 week. Cell populations were analysed by bulk RNA-Seq old adult bone marrow.

first: Vasiliki

last: Symeonidou


title: Two oppositely-chargedsf3b1 mutations cause defective development, impaired immune response, and aberrant selection of intronic branch sites in Drosophila

first: Zhan

last: Ding

address: FengLin 300

institute: CAS Center for Excellence in Molecular Plant Science

summary: Somatic SF3b1 mutations occur in many cancers, and the highly conserved H662 residue is one of the most frequently mutated sites. To address their mechanism on splicing alteration and effects on development, we constructed mutant strains at the corresponding residue H698 in Drosophila using CRISPR-Cas9 system. Two mutations, H698D and H698R, were selected due to their presence in patients and the significantly opposite charges. Both the sf3b1-H698D and –H698R mutant flies exhibit developmental defects including less egg-laying, decreased hatching rates, delayed morphogenesis and shorter lifespan. Interestingly, the H698D mutant has decreased resistance to fungi infection, while the H698R mutant has impaired climbing ability. Further RNA-seq data finds altered expression of immunity response genes and changed alternative splicing of muscle and neural-related genes in the two mutants respectively. Lariat sequencing reveal that the sf3b1-H662 mutations cause aberrant selection of multiple intronic branch sites and the H698R mutant prefers to use upstream branch sites in the alternative splicing changed events. This study provides in vivo evidence from Drosophila to elucidate how the highly conserved SF3b1 cancer mutations alter splicing and their consequences in the development and immune systems.

overall_design: Transcriptional profiles of the 5d adults WT, SF3b1-H698D and -H698R mutant strains

first: Bei

last: Zhang

first: Yong-Zhen


title: Transcriptome expression of human bone marrow mesenchymal stem cell (hBMSCs) during osteogenesis

city: Guangzhou

first: Yiyang

state: Guangdong

address: 74 ZHONGSHAN SECOND ROAD

institute: Sun Yat-Sen University

summary: In this study, we performed the high-throughput sequencing of hBMSCs between day 0 and day 21 during induction of osteogenic differentiation, followed by analysis of the different expression in whole transcriptomes.

overall_design: Bone marrow tissue taken from the volunteers was isolated for hBMSCs. Flow analysis and multidirectional differentiation induction were used to identify stem cell characteristics and differentiation potential of hBMSCs. The third passage of hBMSCs were planted on 6-well plates and cultured in osteogenic differentiation induction medium. The induction medium was changed every three days. At day 0 and day 21, the cells were digested and collected for sequencing.

first: Guping

last: Mao


title: RNAseq analysis of blood from respiratory viruses-infected patients and healthy controls

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

summary: The objective of this study was to understand the shared and unique elements of the host transcriptional response to different viral pathogens. We identified 162 subjects in the US and Sri Lanka with infections due to influenza, enterovirus/rhinovirus, human metapneumovirus, dengue virus, cytomegalovirus, Epstein Barr Virus, or adenovirus. Our dataset allowed us to identify common pathways at the molecular level as well as virus-specific differences in the host immune response. Conserved elements of the host response to these viral infections high-lighted the importance of interferon pathway activation. However, the magnitude of the re-sponses varied between pathogens. We also identified virus-specific responses to influenza, enterovirus/rhinovirus, and dengue infections.

overall_design: Peripheral blood was collected from patients, RNA was isolated and sequenced.


title: Differences between fibroblasts derived from normal and IPF lungs

status: Public on Oct 06 2021

city: Suita

first: Hiroyuki

last: Yamato

state: Osaka

address: 2-2-L5, Yamadaoka

department: General Thoracic Surgery

institute: Osaka University Graduate School of Medicine

summary:
Objective: To evaluate the characteristics of IPF lungs in fibroblasts, we performed RNA-Sequencing of fibroblasts derived from normal and IPF lungs
Method:　NHLF（Normal human lung fibroblast）　and DHLF-IPF (DIPF; Diseased human lung fibroblasts derived from idiopathic pulmonary fibrosis)　were purchased from Lonza (Walkersville, MD, USA) .Total RNA was extracted from fibroblasts (NHLF and DIPF) using an RNeasy® Mini Kit (#74106; Qiagen, Valencia, CA, USA). Preparation of a next-generation sequencing library was performed using a SMARTer® Stranded Total RNA Sample Prep Kit–Pico Input Mammalian (TaKaRa, Shiga, Japan). Sequencing was performed on an Illumina HiSeq 2500 platform in 75-base single-end mode with Illumina Casava 1.8.2 software for base calling. Sequenced reads were mapped to the human reference genome sequence (hg19) using TopHat v.2.0.13 software, in combination with Bowtie 2 v.2.2.3 and SAMtools v.0.1.19.
Result: Of the 26,257 genes analyzed, for NHLF and DHLF-IPF (DIPF), FPKM was required to be greater than or equal to 0.3. Under these conditions, 764 genes were up regulated inDHLF-IPF (DIPF) and 691 genes were down regulated.

overall_design: 2 cell lines; NHLF (Normal human lung fibroblast) and DHLF-IPF (DIPF; Diseased human lung fibroblasts derived from idiopathic pulmonary fibrosis)

first: Yasushi

last: Shintani


title: RNA sequencing of wild type C.elegans exposed to Haptoglossa zoospora for 6 or 12 hours

city: London

first: Michalis

last: Barkoulas

address: Sir Alexander Fleming Building, Imperial College RD

department: Faculty of Natural Sciences

institute: Imperial College London

summary: We aimed to investigate the C. elegans response to Haptoglossa zoospora infection. To this end we performed RNA sequencing using the illumina Hiseq 2500 platform on infected animals at the L4 stage of development after 6hours and 12 hours of pathogen exposure and uninfected animals at the same time points . The sequence reads, generated by Imperial College London sequencing facility (Hammersmith campus) that passed quality controls were aligned to the most recent C. elegans (WBcel235) transcriptome using the pseudoalignment tool Kallisto. The generated abundance files were  analysed using an R pipeline for Sleuth.  Differentially expressed genes with a p value <0.01 and FDR value <0.1 were isolated from the dataset and compared to genes induced in infections by other C. elegans pathogens including the oomycete Myzocytiopsis humicola. The result of this comparison revealed conserved features underlying oomycete detection by C. elegans.

overall_design: RNA sequencing profiles of L4 control or Haptoglossa exposed C. elegans

first: Michael

middle: K

last: Fasseas

first: Manish

last: Grover


title: Hspa1a-regulated gene expression and alternative splicing in mouse cardiomyocytes are tightly related to cardiac hypertrophy

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Regulatory factors play important roles in cardiac hypertrophy by regulating gene expression in cardiomyocytes.HSP70, a heat shock protein encoded by HSPA1A ,is induced by hypertrophic stimulation and then causes cardiac hypertrophy. However, the regulation mechanism of HSP70 in cardiac hypertrophy is unknown. In this study, we established the cardiac hypertrophy mouse model to explore the differentially expressed genes and found Hspa1a was significantly increased in treated samples. Then Hspa1a was overexpressed in mouse cardiac HL-1 cells and we analyzed the changes of transcriptome expression by high throughput sequencing. The results showed that HSPA1A selectively regulates the expression of ncRNAs (Rn7sk,Rmrp), negatively regulates the expression of genes involved in inflammatory and immune response, including Cxcl1，Ccl2，Ccl7,Cxcl5, Fas andC3, which were also validated by RT-qPCR experiment. The HSPA1A-regulated genes and ncRNAs are highly associated with cardiac hypertrophy. Alternative splicing analysis revealed HSPA1A preferred to regulate genes enriched in transcriptional regulation, including Asxl2 and Runx1. These results indicate that the heat shock protein-HSPA1A may play a role in the occurrence and development of myocardial hypertrophy by regulating the expression of immune inflammatory response related pathway genes and ncRNAs related to myocardial hypertrophy.

overall_design: transcriptional analysis of HSPA1A overexpression and control in HL-1 cells

first: Shuai

last: Li

first: Ping

last: Yang


title: Disrupted PGR-B and ESR1 signaling underlies defective decidualization linked to severe preeclampsia

city: valencia

first: Tamara

last: Garrido

address: Narcís Monturiol Estarriol nº11

country: Spain

institute: Igenomix

summary: In the present study, we aimed to discern the preconception decidual transcriptomic signature associated with in vivo defective decidualization in women who suffered sPE in a previous pregnancy. First, we performed a comparative global transcriptional profiling of endometrium from women who developed sPE in a previous pregnancy and from women who never have had sPE. Then, we selected those genes that were significantly deregulated 1.4-fold higher (FDR<0.05) and have an EntrezID code. As a result, we formulate a transcriptional signature associated with defective decidualization composed by 120 genes.

overall_design: A total of 40 non-pregnant women who experienced a previous pregnancy were enrolled in this study for endometrial RNA-sequencing analysis. Endometrial samples were obtained during late secretory phase in 24 women who had developed sPE in a previous pregnancy and in 16 women with no history of sPE with full term (n=8) and preterm pregnancies (n=8) as controls. The experimental design was based on a stratified random sampling with a 70:30 proportion in two cohorts: a training and validation set of samples. The training set of samples was analyzed by RNA-seq to identify the global transcriptomic profiling changes between control (n=12) and sPE (n=17) samples. Finally, targeted analysis of the transcriptional signature was validated in the test set composed of controls (n=4) and sPE (n=7).

last: Garrido-Gomez

first: Nerea

last: Castillo-Marco

first: Mónica

last: Clemente-Ciscar

first: Teresa

last: Cordero

first: Irene

last: Muñoz-Blat

first: Alicia

last: Amadoz

first: Jorge

last: Jimenez-Almazan

first: Rogelio

last: Monfort

first: Reyes

last: Climent

first: Alfredo

last: Perales

first: Carlos

last: Simón


title: Pervasive 3'-UTR isoform switches during mouse oocyte maturation

status: Public on Oct 05 2021

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: Oocyte maturation is the foundation for developing healthy individuals of mammals. Upon germinal vesicle breakdown, oocyte meiosis resumes and the synthesis of new transcripts ceases. To quantitatively profile the transcriptomic dynamics after meiotic resumption throughout the oocyte maturation, we generated transcriptome sequencing data with individual mouse oocytes at three main developmental stages: germinal vesicle (GV), metaphase I (MI), and metaphase II (MII). When clustering the sequenced oocytes, results showed that isoform-level expression analysis outperformed gene-level analysis, indicating isoform expression provided extra information that was useful in distinguishing oocyte stages. Comparing transcriptomes of the oocytes at the GV stage and the MII stage, in addition to identification of differentially expressed genes (DEGs), we detected many differentially expressed transcripts (DETs), some of which came from genes that were not identified as DEGs. When breaking down the isoform-level changes into alternative RNA processing events, we found the main source of isoform composition changes was the alternative usage of polyadenylation sites. With detailed analysis focusing on the alternative usage of 3'-UTR isoforms, we identified, out of 3810 tested genes, 512 (13.7%) exhibiting significant switches of 3'-UTR isoforms during the process of moues oocyte maturation. Altogether, our data and analyses suggest the importance of examining isoform abundance changes during oocyte maturation, and further investigation of the pervasive 3'-UTR isoform switches in the transition may deepen our understanding on the molecular mechanisms underlying mammalian early development.

overall_design: RNA was extracted from individual mouse oocytes at the GV, MI, and MII stages.

first: Yuanlin

last: He

first: Qiuzhen


title: Cumulative in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse Hoxd cluster [cHi-C]

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

summary: We used Capture Hi-C enriching the Hoxd locus and its flanking TADs to study the effects of CRISPR/Cas9-induced CTCF binding sites deletions on chromatin architecture. We analysed wildtype and homozygous mutant E9.5 trunks and E12.5 distal and proximal forelimbs.

first: Ana

last: Amândio

first: Leonardo

last: Beccari

first: Bénédicte

last: Mascrez

first: Jozsef

last: Zakany

first: Sandra

last: Gitto

first: Denis

last: Duboule


title: MALT1-dependent cleavage of HOIL1 modulates canonical NF-kB signaling and inflammatory responsiveness

city: Vancouver

first: Stuart

middle: E

last: Turvey

state: British Columbia

address: A5-122 950 W 28th Avenue

department: Pediatrics

country: Canada

institute: The University of British Columbia

summary: From patient-derived HOIL1-deficient skin fibroblasts transduced with WT and p.Arg165Lys (R/K) HOIL1, we performed differential expression analysis, gene set enrichment, and pathway analyses by RNA-Seq to demonstrate exaggerated activation of inflammatory pathways.

overall_design: Transcriptome profiling of untransduced and WT or p.Arg165Lys (R/K) HOIL1-transduced HOIL1-deficient patient skin fibroblasts in technical triplicate, with or without stimulation (4hrs 10ng/mL IL-1b)

first: Henry

last: Lu

first: Shan-Yu

last: Fung

first: Mehul

last: Sharma

first: Ashish


title: Cumulative in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse Hoxd cluster [RNA-seq]

summary: RNA-seq analysis of the effect of CRISPR/Cas9-induced CTCF binding sites deletions on gene expression. We studied E12.5 distal or proximal forelimbs of wildtype and mutant alleles.